Closed amkram closed 2 years ago
Wow -- it's super cool to imagine Taxonium being using for other species!
The x-scale thing is a good Q. Firstly I definitely need to add some X zoom, pan function, it's just been somewhat tricky and never top priority. But I'm not sure if that 100% addresses this. I think one may always need some way of manually specifying either the scale, as here, or else the initial zoom range for the x axis (which comes to sort of the same thing). This is because there can be outliers, so I think someone probably has to design what things look like initially (i.e. deciding what is an outlier and can be cut off). But i guess if you don't think that is the case then you have the option of automatically setting this value based on the tree.
This PR introduces some changes necessary to build a Taxonium tree for M. tuberculosis.
--x-scale
is added as an optional argument tomatUtils extract --write-taxodium
. This scales the x-values so the tree can be viewed at a desirable scale in Taxonium. This may be a temporary addition that is removed as Taxonium evolves -- I would appreciate @theosanderson's input on this :) The default is set to0.02
for SARS-CoV-2 trees.